public class PeptideProteinMapping extends Object
Constructor and Description |
---|
PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index)
Constructor.
|
PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index,
ArrayList<ModificationMatch> modificationMatches)
Constructor.
|
PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index,
ArrayList<ModificationMatch> modificationMatches,
ArrayList<VariantMatch> variantMatches)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
int |
getIndex()
Returns the index on the protein.
|
ArrayList<ModificationMatch> |
getModificationMatches()
Returns eventual modifications found.
|
static HashMap<String,HashMap<String,ArrayList<Integer>>> |
getPeptideProteinIndexesMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
Returns a map made from the given mappings containing the indexes of the
peptides in the protein sequences indexed by peptide sequence and protein
accession.
|
static HashMap<String,HashSet<String>> |
getPeptideProteinMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
Returns a map made from the given mappings containing protein accessions
for every peptide sequence.
|
static Collection<Peptide> |
getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings,
SequenceMatchingPreferences sequenceMatchingPreferences)
Aggregates the given mapping into a list of peptides.
|
String |
getPeptideSequence()
Returns the peptide sequence.
|
String |
getProteinAccession()
Returns the accession of the protein.
|
ArrayList<VariantMatch> |
getVariantMatches()
Returns eventual variants found.
|
public PeptideProteinMapping(String proteinAccession, String peptideSequence, int index)
proteinAccession
- the accession of the proteinpeptideSequence
- the peptide sequenceindex
- the index on the proteinpublic PeptideProteinMapping(String proteinAccession, String peptideSequence, int index, ArrayList<ModificationMatch> modificationMatches)
proteinAccession
- the accession of the proteinpeptideSequence
- the peptide sequenceindex
- the index on the proteinmodificationMatches
- modification matchespublic PeptideProteinMapping(String proteinAccession, String peptideSequence, int index, ArrayList<ModificationMatch> modificationMatches, ArrayList<VariantMatch> variantMatches)
proteinAccession
- the accession of the proteinpeptideSequence
- the peptide sequenceindex
- the index on the proteinmodificationMatches
- eventual modification matchesvariantMatches
- eventual variant matchespublic String getProteinAccession()
public String getPeptideSequence()
public int getIndex()
public ArrayList<ModificationMatch> getModificationMatches()
public ArrayList<VariantMatch> getVariantMatches()
public static HashMap<String,HashMap<String,ArrayList<Integer>>> getPeptideProteinIndexesMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
peptideProteinMappings
- a list of peptide to protein mappingspublic static HashMap<String,HashSet<String>> getPeptideProteinMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
peptideProteinMappings
- a list of peptide to protein mappingspublic static Collection<Peptide> getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings, SequenceMatchingPreferences sequenceMatchingPreferences)
peptideProteinMappings
- a list of peptides to protein mappingssequenceMatchingPreferences
- the sequence matching preferencesCopyright © 2018. All rights reserved.